ANDREASSEN 4 Flashcards
The DNA damage response (DDR) is critical for maintaining _________ and preventing human diseases such as _________.
genome stability, cancer
The three major prongs of the DNA damage response are:
Cell cycle (checkpoint) arrest, DNA repair, Apoptosis
List three key functions of the DDR
Detecting (sensing) DNA damage, Mediating subsequent signaling that arrests the cell cycle (as appropriate), Coordinately mediating signals that recruit and regulate DNA repair proteins.
The term “DNA damage checkpoint” can refer to the arrest of a particular process such as _________, or to ________ in response to DNA damage.
a block to the firing of new origins, cell cycle arrest at a particular stage (like G2)
Besides its role in maintaining genome stability, the DNA damage response is also important to _________ and _________.
cancer genetics, cancer therapy
DNA-PK, ATM, and ATR are all _________ which are key transducers in DNA damage responses.
PI3K-related protein kinases
ATM and ATR are sometimes called “__________” because deficiency for either of them perturbs certain checkpoints.
checkpoint kinases
ATR and ATM have evolved to mediate and coordinate the response to _________ and _________, respectively.
replication stress, DSBs (double-strand breaks)
Replication stress impedes _________ and can lead to _________.
DNA replication, fork collapse
Fork collapse blocks _________ and can yield _________.
proliferation, DSBs
ATR promotes DNA replication via the _________ checkpoint.
intra S
Besides promoting DNA replication, ATR also recruits _________ necessary to restart stalled replication forks.
HR (homologous recombination) proteins
DSBs must be repaired prior to _________ to ensure _________.
mitotic entry, chromosome integrity
ATM recruits _________ necessary to repair DSBs.
HR proteins
List three examples of replication stress-inducing agents
UV-C, HU (hydroxyurea), MMC (mitomycin C)
List two examples of DSB-inducing agents
IR (ionizing radiation), Topo II inhibitors
The sensor for DSBs is the _________ complex.
MRN (MRE11/Rad50/NBS1)
List three sensors for replication stress
RPA, Rad17, H2AX
ATM and ATR phosphorylate proteins with distinct roles in DNA damage responses, including:
Partner kinases – Chk1/Chk2, Sensors of DNA damage – NBS1, RPA, Rad9, Damage signaling – H2AX, BRCA1, Repair proteins – BLM, FANCI, Apoptosis/G1-S checkpoint – p53
The partner checkpoint kinases for ATM and ATR are _________ and _________, respectively.
CHK2, CHK1
The concept of cell cycle checkpoints was established by _________ and _________ in _________.
Hartwell, Weinert, 1989
Cell cycle checkpoints act to ensure the _________ of cell cycle events.
order
Potential consequences of a defect in checkpoints include _________, _________, and _________.
cell death, increased mutagenesis, infidelity in chromosome segregation
DNA damage can cause checkpoint-dependent arrest of the cell cycle at the _________, within _________, and at _________ prior to mitotic entry.
G1-S transition, S phase (intra-S), G2
Cell cycle arrest in response to DNA damage is mediated by _________ or _________ depending on the type of damage via control of _________.
ATM, ATR, cyclin-dependent kinases (CDKs)
The G1 DNA damage checkpoint acts at the _________ restriction point.
Rb-dependent
Seminal work on p53 and pRb was critical for understanding:
The role of tumor suppressors, Cell cycle control, Cell cycle checkpoints, DNA damage responses, Viral oncogenesis
The MRN complex senses a _________ in chromatin and activates _________ ATM.
conformational change, dimeric
Activated ATM phosphorylates many substrates including its partner, _________.
Chk2
ATM-dependent phosphorylation of _________ (in the MRN complex) recruits/activates more ATM.
NBS1
ATM-dependent phosphorylation of NBS1 is a _________ mechanism that amplifies ATM-dependent signaling.
feedback
DNA damage response signaling events provide access of _________ to compacted chromatin.
DNA repair factors
A critical ATM or ATR target in DSB and replication stress, respectively, is a variant histone ______ (______) present in nucleosomes.
H2A, H2AX
MDC1 recruitment is the basis for subsequent _________ of H2A and H2AX, and further recruitment of DNA repair factors.
polyubiquitination
RNF8 mediates ubiquitination of ______ (and/or ______).
H2A, H1
Writers establish the _________ (acetylation, methylation, phosphorylation, or ubiquitination) on histones.
histone mark
_________ is a “writer” of phosphorylation, while _________ is a polyubiquitin “writer.”
ATM, RNF8
Readers recognize and bind to histones modified with a particular _________ (acetylation, methylation, phosphorylation, or ubiquitination).
mark
_________ is a “reader” of H2AX phosphorylation, and _________ is a “reader” of histone ubiquitination.
MDC1, RAP80
K48-linked polyubiquitination targets proteins for _________.
proteasome-mediated degradation
K63-linked polyubiquitination is involved in the recruitment of _________.
DDR proteins
Signaling through gamma-H2AX and MDC1 coordinates HR: _________ (commitment) and _________ (initiation).
end resection, strand invasion
53BP1 recognizes DNA damage-induced modifications of histones ______ and ______.
H2A, H4
53BP1 promotes _________.
NHEJ (non-homologous end joining)
PTIP and RIF1 block _________ (and HR), which permits binding of ______ proteins and ______ at the damage site to initiate NHEJ.
end resection, Ku, DNA-PK
Potential consequences of a defect in checkpoints include cell death, increased _______, and infidelity in chromosome segregation.
mutagenesis
Work with Xenopus extracts suggests that _______ at the fork continue to spool out ssDNA when damage is encountered.
helicases
The 9-1-1 complex is a _______(shape) that slides until it encounters damage.
ring
Among the chemical inhibitors for DNA-PK, ATM, or ATR, _______ inhibitors look most promising and may be effective as a monotherapy.
ATR
P21 blocks CDK2 cyclin E activity at the _______ transition.
G1-S
The release of _______ allows various cell cycle-related factors to be transcribed, particularly replication or S phase factors.
E2F
Work that focused on p53 and pRb was critical in understanding the function of _______.
tumor suppressors
ATM activates its sensor _______ in response to double-strand breaks.
MRN
Ubiquitin conjugates have a diverse set of functions in cellular signaling, including _______, which is most important for transcriptional regulation.
monoubiquitination
The MRN complex is the sensor for ATM, and one of its components, _______, is an enzyme involved in end resection.
MRE11
___________ is a process that occurs at double-strand breaks and involves the removal of nucleotides from the 5’ ends of the break to create 3’ single-strand overhangs. These overhangs are necessary for homologous recombination to occur.
End resection
True or False: The fact that the MRN complex is involved in both sensing damage and end resection suggests that these two processes are closely linked.
True
ATR ___________ a variety of target proteins that are involved in the DNA damage response, including checkpoint activation, DNA repair, and apoptosis.
phosphorylates
_______ is an example of an effector of apoptosis in the DNA damage response.
FANCI
FANCI is a protein that is involved in the Fanconi anemia pathway, which is a DNA repair pathway that is important for repairing ________________.
interstrand crosslinks
The decision between repairing a double-strand break by non-homologous end joining or homologous recombination may be influenced by the local _______ environment.
chromatin
The 9-1-1 complex is made up of three proteins: Rad9, _____, and Hus1.
Rad1
Fork collapse occurs when the replication fork, the structure that carries out DNA replication, encounters a _______ in the DNA template.
lesion
When fork collapse occurs, DNA replication is ______, and this can lead to cell cycle arrest or cell death.
halted
_______ is a protein that is involved in disassembling the displacement loop if it does not find proper homology during homologous recombination.
BLM
During homologous recombination, a __________ loop (D-loop) is formed.
displacement
BLM is thought to help disassemble the ________ if it does not find proper homology with the template. This helps to prevent the formation of non-homologous recombination products, which can lead to genomic instability.
D-loop
Check1 phosphorylates CDC25A, leading to its _______, and thereby maintaining the inhibitory phosphorylation on CDK2.
degradation
True or False: CDK2 is a CDK that is involved in promoting the transition from G1 to S phase.
True
Ataxia telangiectasia and Nijmegen breakage syndrome are both rare genetic disorders that are characterized by a defect in the _______________.
DNA damage response (DDR)
